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Microbial De novo Sequencing

De novo sequencing can sequence the genome of a species without any reference genome information, splice and assemble it by bioinformatics analysis methods, and obtain the genome sequence map of the species, to promote the follow-up research of the species. It offers reference genome assembly for rarely studied species. Using de novo sequencing to obtain the genomic information of microbes provides a fresh start for exploring the genetic structure and functions, studying the evolutionary origin of microbial populations, as well as developing potential applications of these abundant microbes in medicine, disease, agriculture, and the environment.


Novogene offers de novo sequencing services using both PacBio/Nanopore and Illumina platforms. We provide multifaceted sequencing services including genome survey, draft map, complete map, and fine map tailored to different research needs. For each project, our scientists will design the best sequencing strategy utilizing an optimal combination of short reads and long-range sequencing information to achieve the most comprehensive de novo assembly results for your genome of interest.

Benefits

Highly experienced
Highly experienced

We have completed numerous microbial de novo sequencing projects, resulting in publications in top-tier journals.

Largest sequencing capacity
Largest sequencing capacity

We offer world-leading sequencing capacity, delivering high-quality data with fast turnaround and cost efficiency.

In-depth data mining
In-depth data mining

We provide complete solutions for analyzing individual variation and population evolution to address key biological questions.

Accuracy
Accuracy

Creates accurate reference sequences, even for complicated or polyploid genomes.

Applications

For individual research

Virulence Research

Aims to elucidate the specific molecular mechanisms by which a pathogen invades a host and causes disease.

Drug Resistance Mechanism

Focuses on how microbes evolve mechanisms, such as genetic mutations or acquiring resistance genes, to evade the effects of antimicrobial drugs.

Molecular Markers

Involves identifying specific DNA sequences or proteins to rapidly and accurately identify the species or strain of a pathogen.

Vaccine Development

The process of designing safe antigenic components or attenuated pathogens to stimulate a protective immune response for preventing infection.

For Population Research

Evolutionary Relationship

Uses genetic sequence comparison to reveal the genetic relatedness and evolutionary history among different strains or species.

Population Size

Estimates the effective population size of a microbial community in a given environment to understand its genetic diversity and evolutionary potential.

Epidemiology

Tracks the transmission pathways, scale, patterns, and risk factors of infectious diseases to inform public health control strategies.

Microbial Evolution

Studies the adaptive changes in the genome and phenotype of microbial populations over time in response to environmental or host pressures.

Specifications

Sample Requirements

Sample amounts are listed for reference only. Download the Sample Submission Guidelines to learn more. For detailed information, please contact us with your customized requests.

Platform TypeSample TypeAmount (Qubit®)Purity
Illumina NovaSeqGenomic DNA≥ 200 ngA260/280=1.8-2.0
no degradation,
no degradation,
no contamination
PacBio Revio DNA HiFi libraryHMW Genomic DNA(Bacteria and Fungus)≥ 1.5 μg
(Concentration ≥ 50 ng/μL)
A260/280=1.75-2.0;
A260/230=1.3-2.6;
*NC/QC=1.0-2.2;
Fragments should be  ≥ 20 kb
Nanopore PromethIONHMW Genomic DNA(Bacteria and Fungus)≥ 6 μg
(Concentration ≥ 60 ng/μL)
A260/280=1.7-2.2;
A260/230=1.3-2.6;
*NC/QC=0.95-3.00
Fragments should be ≥ 20 kb
* NC/QC: NanoDrop concentration/Qubit concentration

Sequencing and Analysis

Recommended data outputs and analysis contents displayed are for reference only. For detailed information, please contact us with your customized requests.

Platform TypeIllumina NovaSeqPacBio Revio
Read LengthPaired-end 150 bpN50>15 kb, long read lengths up to 25 kb
Recommended Sequencing Depth≥ 50x for bacterial and fungal genomes≥ 0.5G HiFi reads for bacterial genomes
≥ 50X for fungal genomes
Data Analysis· Bacterial and Fungal Draft Map
· Standard Analysis
· Data quality control
· Genome preliminarily assembly
· Genome component analysis
· gene structure prediction
· repetitive sequences
· non-coding RNAs
· Gene function annotation
· Bacteria Complete Map
· Standard Analysis
· Data quality control
· Genome assembly
· Genome component analysis
· Repeat annotation
· Coding gene annotation
· ncRNA annotation
· Gene function annotation
· GO annotation
· KEGG annotation
· COG annotation
· NR annotation
· TCDB annotation
· Pfam annotation
· Swiss-Prot annotation
· Whole-genome circular map
· Fungus Fine Map
· Standard Analysis
· Data quality control
· Genome survey
· Genome assembly
· Genome component analysis
· Repeat annotation
· Coding gene annotation
· ncRNA annotation
· Gene function annotation
· GO annotation
· KEGG annotation
· NR annotation
· KOG annotation
· Pfam annotation
· Swiss-Prot annotation

Novogene Workflow of Microbial De novo Sequencing

Novogene Workflow of Microbial De novo Sequencing

Demo Results

Background

Ready to Start Your Project?

Our platform offers tailored solutions for

your unique experimental needs, ensuring a seamless experience from project design to data delivery.